Atlas2 integrated SNP/Indel calling pipeline
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Atlas2 is a suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in Whole Exome Capture Sequencing (WECS) data. |
Atlas-Link
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Atlas-Link links and orients genome sequence contigs into scaffolds quickly and accurately using mate-pair information. Atlas-Link can also be used to superscaffold existing genome assemblies with data from new sequencing technologies. |
Atlas-GapFill
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For each gap in a genome assembly, Atlas-GapFill identifies gap-associated sequence reads, performs local sequence assembly of the data and fills that gap with the newly assembled sequence contig. |
SNPTools
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A suite of software tools that enable integrative SNP analysis in sequencing data with large cohorts. It employs a novel imputation engine to achieve highly accurate genotype calls in a efficient way. |
Atlas Whole Genome Assembly Suite
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A suite of software tools for the assembly of large genomes. |
Atlas Visualization Tools
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Visualization tools in support of large-scale assembly. MegaDot - A large-scale dot plotter bcm-ace-plots - A tool to display contig template coverage, read coverage, quality, and high quality discrepencies atlas-readpainter - A multiple alignment to reference tool |
bang
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A fast, easy to use, repeat supressing search tool. |
CBT++
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A collection of C++ classes to aid the development of computational biology applications. |
BCM Trace Viewer
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A Java application/applet to display .scf traces and phred quality values. |
BCM Java Alignment Viewer
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A Java application/applet to view sequence alignment files. |
PASH comparison method
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An efficient large-scale sequence comparison method that uses positional hashing. |
SimPed
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SimPed quickly generates haplotype and/or genotype data for pedigrees. |